Medical Computing > OWL

Introduction to OWL Web Ontology Language for Medical and Biosciences Applications (Continued)

Contents

Summary

This article introduced the OWL Web ontology language using examples from medicine and biosciences.  One of the problems with OWL at present is the relative lack of tools for users who are not expert in data modeling with OWL.  In particular, the subject matter experts who would contribute content to ontologies must also be knowlegable about OWL, which is a barrier to creation of ontologies.  A user interface generated from the BioPax Level 2 ontology was demonstrated.  However, while OWL externalizes domain knowledge out of the source code it is difficult to generate an end-user interface that is not simply a relection of class structure.

About Author

Alex Amies is a software engineer.  He has a BS in Computer Science from the University of New South Wales and an MS in Engineering from Stanford University.  He can be contacted at alexamies@gmail.com.

Related Reading

  1. Alex Amies, 2006.  Introduction to Data Modeling for Physiology: The Human Endocrine System.
  2. Alex Amies, 2006.  Introduction to Extensible Markup Language for Chemistry and Biosciences.

References

  1. World Wide Web Consortium (W3C) 2004.  RDF Primer, W3C Recommendation 10 February 2004 at www.w3.org/TR/rdf-primer/.
  2. W3C 2004.  RDF/XML Syntax Specification (Revised), W3C Recommendation 10 February 2004 at www.w3.org/TR/rdf-syntax-grammar/.
  3. W3C 2004. OWL Web Ontology Language Reference.  W3C Recommendation 10 February 2004 at www.w3.org/TR/owl-ref/.
  4. W3C 2004.  OWL Web Ontology Language Overview, W3C Recommendation 10 February 2004 at www.w3.org/TR/2004/REC-owl-features-20040210/.
  5. W3C 2004.  OWL Web Ontology Language Guide, W3C Recommendation 10 February 2004 at www.w3.org/TR/2004/REC-owl-guide-20040210/.
  6. OWL Web Ontology Language Semantics and Abstract Syntax, W3C Recommendation 10 February 2004 at www.w3.org/TR/owl-semantics/.
  7. Internet Engineering Task Force (IETF), 1998.  Request for Comments 2396: Uniform Resource Identifiers (URI): Generic Syntax at www.ietf.org/rfc/rfc2396.txt.
  8. Natalya F. Noy  and Deborah L. McGuinness, 2001. Ontology Development 101: A Guide to Creating Your First Ontology at www.ksl.stanford.edu/people/dlm/papers/ontology101/ontology101-noy-mcguinness.html.
  9. Dublin Core Metadata at home page, http://dublincore.org/.
  10. The Karlsruhe Ontology and Semantic Web Tool Suite at kaon.semanticweb.org.
  11. Ontoknowledge Home Page at www.ontoknowledge.org/.
  12. University of Maryland Simple HTML Ontology Extensions (SHOE) home page at www.cs.umd.edu/projects/plus/SHOE/.
  13. KR Home Page at kr.org/.
  14. James Hendler, Tim Berners-Lee, and Eric Miller 2002.  Integrating Applications on the Semantic Web,  Journal of the Institute of Electrical Engineers of Japan, Vol 122(10), October, 2002, p. 676-680 at www.w3.org/2002/07/swint.
  15. Stanford University, Protégé ontology editor and knowledge-base framework at protege.stanford.edu/.  The Protégé API Javadoc is at protege.stanford.edu/doc/pdk/api/index.html, the Protégé-OWL Programmers Guide is at protege.stanford.edu/plugins/owl/api/guide.html, and the Protégé-OWL API Javadoc is at protege-owl.sourceforge.net/javadoc/.
  16. BioPAX open source project at www.biopax.org/, BioPAX – Biological Pathways Exchange Language, Level 2, Version 1.0 Documentation at www.biopax.org/release/biopax-level2-documentation.pdf.
  17. University Of Manchester 2004.  OWLDoc home page at www.co-ode.org/downloads/owldoc/co-ode-index.php.
  18. US National Library of Medicine, Unified Medical Language System at www.nlm.nih.gov/research/umls/umlsmain.html.  The Knowledge Source Server Logon is at umlsks.nlm.nih.gov/kss/servlet/Turbine/template/admin,user,KSS_login.vm.
  19. Stanford KSL Network Services, ontology software tools at http://www-ksl-svc.stanford.edu:5915/.
  20. Stanford University, Chimæra ontology research project at www.ksl.stanford.edu/software/chimaera/.
  21. The Open Biomedical Ontologies at http://obo.sourceforge.net/.
  22. Gene Ontology page at www.geneontology.org/.
  23. W3C 2006. SPARQL Query Language for RDF: W3C Candidate Recommendation 6 April 2006 at www.w3.org/TR/rdf-sparql-query/.
  24. The National Center for Biomedical Ontology web site at bioontology.org/.
  25. The European Bioinformatics Institute has a Ontology Lookup Service at www.ebi.ac.uk/ontology-lookup/ and software tools.
  26. Generic Model Organism Database Construction Set open source project at gmod.sourceforge.net/ has a number of Java tools for bioinformatics ontology projects.
  27. Standards and Ontologies for Functional Genomics at http://www.sofg.org/.
  28. MGED Open Source Projects at http://mged.sourceforge.net/.
  29. Plant Ontology™ Consortium at http://www.plantontology.org/.
  30. The Trial Bank Project at rctbank.ucsf.edu/.
  31. W3C Extensible Stylesheet Language Family (XSL) web page at www.w3.org/Style/XSL/.  The XML Path Language (XPath) 2.0: W3C Candidate Recommendation 3 November 2005 is at www.w3.org/TR/xpath20/.
  32. W3C 2006.  SPARQL Query Language for RDF W3C Candidate Recommendation 6 April 2006 at www.w3.org/TR/rdf-sparql-query/.
  33. Philip McCarthy 2005.  Search RDF data with SPARQL at www-128.ibm.com/developerworks/library/j-sparql/.
  34. Philip McCarthy 2004.  Introduction to Jena at www-128.ibm.com/developerworks/java/library/j-jena/.
  35. ARQ (A SPARQL Processor for Jena) is an open source project at http://jena.sourceforge.net/ARQ/.
  36. SPARQLer - An RDF Query Demo at http://www.sparql.org/query.html.
  37. Matthias Samwald, Case Western Reserve University, Psychoactive Drug Screening Program Ki database at kidb.cwru.edu/.


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© Alex Amies 2006